We have developed various techniques for protein separation and its characterization by mass spectrometry. Our recent development of protein-chip, a high-throughput, highly sensitive and largely automatic tool for protein functional network is well-recognized. Using these techniques, we are studying the structure and function of various proteins including human disease-associated proteins. Simultaneously, our research is focused on post-translational modifications and their function in large protein complex such as 26S proteasome, ubiquitin ligase and ribosome.